rs387907016
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PVS1PS1_ModeratePM2PP5
The NM_001199799.2(ILDR1):c.3G>A(p.Met1?) variant causes a start lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000687 in 1,454,940 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (no stars).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
ILDR1
NM_001199799.2 start_lost
NM_001199799.2 start_lost
Scores
5
7
3
Clinical Significance
Conservation
PhyloP100: 2.13
Genes affected
ILDR1 (HGNC:28741): (immunoglobulin like domain containing receptor 1) This gene encodes a protein that contains an immunoglobulin-like domain. The encoded protein may function as a multimeric receptor at the cell surface. The expression of this gene may be a diagnostic marker for cancer progression. Alternatively spliced transcript variants encoding multiple protein isoforms have been observed for this gene. [provided by RefSeq, Dec 2010]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 13 ACMG points.
PVS1
?
Start lost variant, no new inframe start found.
PS1
?
Another start lost variant in NM_001199799.2 (ILDR1) was described as [Pathogenic] in ClinVar as 3253316
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 3-122022075-C-T is Pathogenic according to our data. Variant chr3-122022075-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 30797.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-122022075-C-T is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ILDR1 | NM_001199799.2 | c.3G>A | p.Met1? | start_lost | 1/8 | ENST00000344209.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ILDR1 | ENST00000344209.10 | c.3G>A | p.Met1? | start_lost | 1/8 | 1 | NM_001199799.2 | P2 | |
ILDR1 | ENST00000273691.7 | c.3G>A | p.Met1? | start_lost | 1/7 | 1 | A2 | ||
ILDR1 | ENST00000393631.5 | c.3G>A | p.Met1? | start_lost | 1/6 | 1 | |||
ILDR1 | ENST00000642615.1 | c.3G>A | p.Met1? | start_lost, NMD_transcript_variant | 1/8 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome AF: 6.87e-7 AC: 1AN: 1454940Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 723056
GnomAD4 exome
AF:
AC:
1
AN:
1454940
Hom.:
Cov.:
30
AF XY:
AC XY:
1
AN XY:
723056
Gnomad4 AFR exome
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
Alfa
AF:
Hom.:
ClinVar
Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:2
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Autosomal recessive nonsyndromic hearing loss 42 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 11, 2011 | - - |
Hearing loss, autosomal recessive Pathogenic:1
Likely pathogenic, no assertion criteria provided | research | University of Washington Center for Mendelian Genomics, University of Washington | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Benign
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Benign
D
LIST_S2
Uncertain
D;.;D;D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D;D;D
MetaSVM
Uncertain
T
MutationTaster
Benign
D;D;D
PROVEAN
Benign
N;N;N;N
REVEL
Uncertain
Sift
Uncertain
D;T;D;D
Sift4G
Pathogenic
D;D;.;D
Polyphen
P;P;P;P
Vest4
MutPred
Loss of ubiquitination at K5 (P = 0.0603);Loss of ubiquitination at K5 (P = 0.0603);Loss of ubiquitination at K5 (P = 0.0603);Loss of ubiquitination at K5 (P = 0.0603);
MVP
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at